Poaceae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA380659 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5406160_1.fastq.gz | Fastqsanger.gz | |||
| SRR5406160_2.fastq.gz | Fastqsanger.gz | |||
| SRR5406170_1.fastq.gz | Fastqsanger.gz | |||
| SRR5406170_2.fastq.gz | Fastqsanger.gz | |||
| SRR5406180_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 92 |
Similar Datasets
Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4401 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4401/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)
2012-04-04 | E-MTAB-4400 | biostudies-arrayexpress
Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4400 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4400/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)
2012-04-04 | E-MTAB-4401 | biostudies-arrayexpress
Project description:Despite the economic importance of grasses as food, feed and energy crops, little is known about the genes that control their cell wall synthesis, assembly and remodelling. Here we provide a detailed transcriptome analysis that allowed the identification of genes involved in grass cell wall biogenesis. Differential gene-expression profiling, using maize oligonucleotide arrays, was used to identify genes differentially expressed between an elongating internode, containing cells exhibiting primary cell wall synthesis, and an internode that had just ceased elongation and in which many cells were depositing secondary cell wall material. This is one of only few studies specifically aimed at the identification of cell wall-related genes in grasses. Analysis identified new candidate genes for a role in primary and secondary cell wall-related processes in grasses. The results suggest that many proteins involved in cell wall-related processes during normal development are also recruited during defence-related cell wall remodelling events. The data presented provide a platform for future studies in which candidate genes can be tested for involvement in cell wall processes through forward and reverse genetic-based approaches, contributing towards a better understanding of cell wall biogenesis and its regulation in grasses.
2011-03-06 | GSE24014 | GEO
Project description:Cell-Specific Image-guided Transcriptomics of Ischemic Acute Kidney Injury
| PRJNA550256 | ENA
Project description:Due to its small and sequenced genome, short generation time, efficient transformation and increasing genetic resources, Brachypodium distachyon is an emerging model for grasses. Despite this, data capturing gene expression patterns across different organs and developmental stages is missing. We have generated a comprehensive gene expression atlas for Brachypodium, capturing 9 different organs and developmental stages
2017-06-03 | E-MTAB-5491 | biostudies-arrayexpress
Project description:Genome-wide maps of cytosine methylation, cytosine hydroxylmethylation and small non coding RNAs in mouse ES cells and upon guided differentiation to mesoendoderm cells. Mouse embryonic stem cells (E14) were guided differentiated into mesoendoderm lineages by activin-A induction. cells in three time points (day0, day4 and day6) were collected. The genome-wide studies on three cell types were summerized as following: cytosine methylation data were generated using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq); DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Biotechnol. 2011, 29, 68-72). E14 Day0 data for MRE-seq and MeDIP-seq are released first in previous publication and included in prior series GSE36114 ChIP-seq, 5-hmC-seq, MeDIP-Seq, MRE-Seq, ncRNA-Seq, and RNA-seq on activin-induced differentiating ES cells at 3 time points.
2012-09-22 | E-GEOD-38596 | biostudies-arrayexpress
Project description:We used ChIP-seq to assess how abolition of KRAB binding by KAP1 (through structure-guided mutations in the KAP1-KRAB binding interface) changed the distribution of KAP1 on chromatin genome-wide.
2022-10-10 | GSE215015 | GEO
Project description:Despite the economic importance of grasses as food, feed and energy crops, little is known about the genes that control their cell wall synthesis, assembly and remodelling. Here we provide a detailed transcriptome analysis that allowed the identification of genes involved in grass cell wall biogenesis. Differential gene-expression profiling, using maize oligonucleotide arrays, was used to identify genes differentially expressed between an elongating internode, containing cells exhibiting primary cell wall synthesis, and an internode that had just ceased elongation and in which many cells were depositing secondary cell wall material. This is one of only few studies specifically aimed at the identification of cell wall-related genes in grasses. Analysis identified new candidate genes for a role in primary and secondary cell wall-related processes in grasses. The results suggest that many proteins involved in cell wall-related processes during normal development are also recruited during defence-related cell wall remodelling events. The data presented provide a platform for future studies in which candidate genes can be tested for involvement in cell wall processes through forward and reverse genetic-based approaches, contributing towards a better understanding of cell wall biogenesis and its regulation in grasses. The experiment consisted of six biological replicates (internode 9 and internode 13 were harvested from six maize plants). Dye-swaps were performed (in 3 slides, internode 9 RNA was labelled with Cy3 and internode 13 RNA was labelled with Cy5; in 3 other slides, internode 13 RNA was labelled with Cy3 and internode 9 RNA was labelled with Cy5).
2011-03-06 | E-GEOD-24014 | biostudies-arrayexpress
Project description:comparative transcriptomics of two temperate C3 bioenergy and forage grasses under water stress
| PRJEB16763 | ENA
Project description:Leymus chinensis strain:Poaceae Transcriptome or Gene expression
| PRJNA230274 | ENA